| 824cfde4 |
## IMPORTANT
- move IRanges and oligoClasses back to Suggests? BC moved them to
Depends just to get rid of annoying warnings while transitioning.
|
| 3620e6b1 |
#####################################
### FOR CRLMM
#####################################
|
| f32a09dd |
- Add RS ids to annotation packages
|
| 3620e6b1 |
- Allele plots
- M v S plots
|
| 5fcfed7d |
R. Scharpf (after next release)
- crlmm should return a SnpSet object with elements A, B, calls, and
confs in the assayData when save.it=TRUE. These objects can be very
big, so...
- crlmm function should have an option to return nothing and write to
file a SnpSet object for each chromosome. This would help the copy
number part that runs by chromosome
|
| f32a09dd |
|
| cd3930b6 |
B Carvalho
|
| 5fcfed7d |
- crlmm should return results in CHP files
***********************************************************
* *
* FOR CNRMA *
* *
***********************************************************
o Bias adjustment for X chromosome
o Adjust nu for altered copy number (crosshyb)
o Should store parameters in something besides the featureData slot
- Perhaps add a matrix slot for parameters and a slot for batch.
- Need accessors
- how to store parameters for chromosome X (should be nu_A_male,
nu_A_female, etc.)?
o Provide a SNP- and sample-specific estimate of the variance for
computing emission probabilities. (Currently, only SNP-specific)
(DONE -- version 1.3.10
|
| cd3930b6 |
|
| 5fcfed7d |
o Allow a copy-neutral ROH state by not having an equal prior on the
ellipses. For instance,
|
| b9c71726 |
|
| 5fcfed7d |
normal state: 1/4 AA, 1/2 AB, 1/4 BB
copy-neutral ROH: (1-epsilon)/2 AA, epsilon AB, (1-epsilon)/2
BB
|
| b9c71726 |
|
| 5fcfed7d |
o Define a class that contains settings for genotyping/copynumber estimation
|
| b9c71726 |
|
| 38fb1b80 |
|
| f8af2fff |
|
